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The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold
Author(s) -
Qiu Yang,
Tereshko Valentina,
Kim Youngchang,
Zhang Rongguang,
Collart Frank,
Yousef Mohammed,
Kossiakoff Anthony,
Joachimiak Andrzej
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20590
Subject(s) - aquifex aeolicus , histone , crystallography , hyperthermophile , histone octamer , antiparallel (mathematics) , sedimentation equilibrium , chemistry , biology , nucleosome , biochemistry , biophysics , archaea , dna , escherichia coli , physics , ultracentrifuge , gene , magnetic field , quantum mechanics
The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus , has been determined to 1.9 Å by using multi‐wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone‐like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z‐score 8.1 and RMSD 3.6 Å over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross‐shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone‐like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper. Proteins 2006. © 2005 Wiley‐Liss, Inc.